Diff of the two buildlogs: -- --- b1/build.log 2025-03-14 21:19:15.764501214 +0000 +++ b2/build.log 2025-03-14 21:23:36.692864289 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Mar 14 08:59:11 -12 2025 -I: pbuilder-time-stamp: 1741985951 +I: Current time: Fri Apr 17 17:42:18 +14 2026 +I: pbuilder-time-stamp: 1776397338 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying sphinx.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1830931/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 17 03:42 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c8ee5e80bec34930a2482241e18c8f66' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1830931' - PS1='# ' - PS2='> ' + INVOCATION_ID=6d361b4b1c82436c948c5dc852c3fff7 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1496209 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/pbuilderrc_nw6y --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/b1 --logfile b1/build.log salmon_1.10.2+ds1-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/pbuilderrc_q0w2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/b2 --logfile b2/build.log salmon_1.10.2+ds1-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1830931/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -399,7 +431,7 @@ Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 rapmap-dev all 0.15.0+dfsg-4 [193 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 sphinx-doc all 8.1.3-5 [3487 kB] -Fetched 154 MB in 8s (18.3 MB/s) +Fetched 154 MB in 5s (30.7 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19785 files and directories currently installed.) @@ -1140,8 +1172,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Mar 14 21:04:13 UTC 2025. -Universal Time is now: Fri Mar 14 21:04:13 UTC 2025. +Local time is now: Fri Apr 17 03:43:04 UTC 2026. +Universal Time is now: Fri Apr 17 03:43:04 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4.1+b2) ... @@ -1349,7 +1381,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/salmon-1.10.2+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../salmon_1.10.2+ds1-1_source.changes +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/salmon-1.10.2+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../salmon_1.10.2+ds1-1_source.changes dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 1.10.2+ds1-1 dpkg-buildpackage: info: source distribution unstable @@ -1504,7 +1540,7 @@ TBB_LIBRARIES = TBB_LIB_INSTALL_DIR = TBBGLOBS = --- Configuring done (14.9s) +-- Configuring done (2.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -1524,185 +1560,266 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend -make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend +make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make 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src/CMakeFiles/salmon_core.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake "--color=" -make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake "--color=" -make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend +make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend +make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake "--color=" -make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src 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'/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build -[ 1%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -MF CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o.d -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c 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external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o +[ 9%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o +[ 10%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o +[ 11%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT 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external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -MF CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o.d -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp +[ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o +[ 20%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o +[ 20%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o +[ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o +[ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o +[ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT 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-I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type 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CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c +[ 33%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c 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/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp -[ 25%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp -[ 26%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder 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-Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/xxhash.c -cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C -cc1: warning: command-line option '-Wno-deprecated-copy' is valid for C++/ObjC++ but not for C -[ 27%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp -[ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -MF CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o.d -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/TranscriptGroup.cpp -[ 29%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp -[ 30%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -[ 31%] Built target ksw2pp_sse4 +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse 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-Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/jellyfish/mer_dna.cc +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp +cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C +cc1: warning: command-line option '-Wno-deprecated-copy' is valid for C++/ObjC++ but not for C +[ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o +[ 35%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 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/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -MF CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o.d -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/TranscriptGroup.cpp +[ 36%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -MF CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o.d -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp -[ 33%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o +[ 37%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o -MF CMakeFiles/puffer.dir/edlib.cpp.o.d -o CMakeFiles/puffer.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/edlib.cpp +[ 38%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o -MF CMakeFiles/puffer.dir/Util.cpp.o.d -o CMakeFiles/puffer.dir/Util.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp +[ 39%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 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-static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -MF CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o.d -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/GenomicFeature.cpp -[ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o +[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -MF CMakeFiles/salmon_core.dir/VersionChecker.cpp.o.d -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/VersionChecker.cpp +[ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -MF CMakeFiles/puffer.dir/rank9sel.cpp.o.d -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9sel.cpp +[ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -MF CMakeFiles/puffer.dir/rank9b.cpp.o.d -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9b.cpp +[ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp +[ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp +[ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 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/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -MF CMakeFiles/puffer.dir/PufferfishValidate.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp +[ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 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CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp +[ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 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/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonExceptions.cpp +[ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp +[ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp +[ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp +[ 52%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp +[ 53%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type 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-DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp +[ 55%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferFS.cpp make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 34%] Built target ksw2pp_sse2 -[ 35%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp -[ 36%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp -[ 37%] Linking CXX static library libntcard.a +[ 56%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context 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-Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/xxhash.c +cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C +[ 58%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SGSmooth.cpp +[ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp +[ 59%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/metro/metrohash64.cpp +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +[ 59%] Built target ksw2pp_sse2 +[ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp +[ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp +[ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG 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-Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp:1: +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +[ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +[ 63%] Built target ksw2pp_basic +[ 64%] Linking CXX static library libntcard.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake +[ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/metro/metrohash64.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 /usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o /usr/bin/ranlib libntcard.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 38%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp -[ 38%] Built target ntcard -[ 39%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp -[ 39%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp -[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp -[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp +[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp +[ 66%] Built target ntcard +make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend +make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build +make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +[ 67%] Linking CXX static library libksw2pp.a +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1711,33 +1828,119 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 40%] Built target ksw2pp_basic -[ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o -MF CMakeFiles/puffer.dir/edlib.cpp.o.d -o CMakeFiles/puffer.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/edlib.cpp -make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend -make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build -make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 42%] Linking CXX static library libksw2pp.a -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-14" qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/gcc-ranlib-14" libksw2pp.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 42%] Built target ksw2pp -[ 43%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishLossyIndex.hpp:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp:7: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +[ 67%] Built target ksw2pp +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp:9: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBaseIndex.hpp:14, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp:1: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishSparseIndex.hpp:13, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp:10: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:14: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp:15: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp:13: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp:1: + from /build/reproducible-path/salmon-1.10.2+ds1/include/SimplePosBias.hpp:4, + from /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o -MF CMakeFiles/puffer.dir/Util.cpp.o.d -o CMakeFiles/puffer.dir/Util.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; @@ -1746,8 +1949,8 @@ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp:9: + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1759,8 +1962,7 @@ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBaseIndex.hpp:14, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp:1: + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp:16: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1769,11 +1971,15 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp: In function 'std::vector get_kmers(const std::string&, uint32_t)': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: unused parameter 'k' [-Wunused-parameter] + 25 | std::vector get_kmers(const std::string& fasta_file, uint32_t k) { + | ~~~~~~~~~^ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishLossyIndex.hpp:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp:7: + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp:6: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1782,17 +1988,22 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -MF CMakeFiles/salmon_core.dir/StadenUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/StadenUtils.cpp -[ 45%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -MF CMakeFiles/puffer.dir/rank9sel.cpp.o.d -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9sel.cpp -[ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishSparseIndex.hpp:13, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp:10: + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp:2: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:5: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1804,7 +2015,47 @@ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp:1: + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemCollector.hpp:6, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp:1: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemChainer.hpp:8, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp:2: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp:35: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1813,10 +2064,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 47%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -MF CMakeFiles/puffer.dir/rank9b.cpp.o.d -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9b.cpp -[ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -MF CMakeFiles/puffer.dir/PufferfishValidate.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:27, @@ -1829,8 +2076,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 49%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' @@ -1938,8 +2183,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonExceptions.cpp /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -1996,171 +2239,97 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o -MF CMakeFiles/puffer.dir/PufferfishStats.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp:15: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 52%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonStringUtils.cpp -[ 53%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp -[ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp:16: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SimplePosBias.hpp:4, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp:1: -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 55%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SGSmooth.cpp -[ 55%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/metro/metrohash64.cpp -[ 55%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.2+ds1/include/UtilityFunctions.hpp:4, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SBModel.hpp:6, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp:1: -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 56%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:14: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp:13: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp: In function 'std::vector get_kmers(const std::string&, uint32_t)': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: unused parameter 'k' [-Wunused-parameter] - 25 | std::vector get_kmers(const std::string& fasta_file, uint32_t k) { - | ~~~~~~~~~^ -[ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp:6: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp:18: -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp: In function 'bool alevin::utils::extractBarcode(std::string&, std::string&, ProtocolT&, std::string&) [with ProtocolT = alevin::protocols::SciSeq3; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:350:104: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 350 | if (pt.anchorPos != std::string::npos && ( pt.anchorPos == pt.maxHairpinIndexLen || pt.anchorPos == pt.maxHairpinIndexLen -1) // only 2 possible values of pt.anchorPos - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferFS.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8, - from /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp:3: -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 60%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/xxhash.c -cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]' + 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2817 | for (destructive_iterator it = ht.destructive_begin(); + | ~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2948 | _move_from(mover, ht, min_buckets_wanted); + | ^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); + | ^~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3278 | if (_resize_delta(1)) + | ^~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' + 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; + | ~~~~~~~~~~~~~~~~~~^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here + 466 | template class RefSeqConstructor; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] + 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } + | ^~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' + 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); + | ^~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' + 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; + | ~~~~~~~~~~~~~~~~~~^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here + 466 | template class RefSeqConstructor; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' + 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; + | ~~~~~~~~~~~~~~~~~~^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here + 466 | template class RefSeqConstructor; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' @@ -2268,8 +2437,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -2326,17 +2493,164 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:5: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] +In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:4: +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' + 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]' + 2817 | for (destructive_iterator it = ht.destructive_begin(); + | ~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]' + 2948 | _move_from(mover, ht, min_buckets_wanted); + | ^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]' + 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); + | ^~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' + 3278 | if (_resize_delta(1)) + | ^~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here + 264 | duplicateNames[dupInfo.txId].push_back(processedName); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' is deprecated [-Wdeprecated-copy] + 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } + | ^~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' + 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); + | ^~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here + 264 | duplicateNames[dupInfo.txId].push_back(processedName); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]' + 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2817 | for (destructive_iterator it = ht.destructive_begin(); + | ~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2948 | _move_from(mover, ht, min_buckets_wanted); + | ^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); + | ^~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3234:9: required from 'std::pair::ne_iterator, bool> spp::sparse_hashtable::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparsetable::ne_iterator = spp::Two_d_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]' + 3234 | _resize_delta(1); // adding an object, grow if need be + | ^~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:4225:73: required from 'std::pair::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator, bool> spp::sparse_hash_set::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparse_hashtable::const_iterator = spp::Two_d_iterator, const spp::sparsegroup, spp::libc_allocator > >*, const std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]' + 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:490:26: required from here + 490 | auto it = dset.insert(dname); + | ~~~~~~~~~~~^~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] + 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } + | ^~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::__cxx11::basic_string; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::__cxx11::basic_string*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' + 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); + | ^~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here + 264 | duplicateNames[dupInfo.txId].push_back(processedName); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, + from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp:18: +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, + from /build/reproducible-path/salmon-1.10.2+ds1/include/UtilityFunctions.hpp:4, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SBModel.hpp:6, + from /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp:1: +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp: In function 'bool alevin::utils::extractBarcode(std::string&, std::string&, ProtocolT&, std::string&) [with ProtocolT = alevin::protocols::SciSeq3; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:350:104: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 350 | if (pt.anchorPos != std::string::npos && ( pt.anchorPos == pt.maxHairpinIndexLen || pt.anchorPos == pt.maxHairpinIndexLen -1) // only 2 possible values of pt.anchorPos + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, + from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8, + from /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp:3: +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >; reference = std::pair, std::vector >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char]' @@ -2497,183 +2811,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemCollector.hpp:6, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp:1: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 63%] Linking CXX static library libgraphdump.a -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 -/usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -/usr/bin/ranlib libgraphdump.a -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 63%] Built target graphdump -[ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemChainer.hpp:8, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp:2: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:4: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' - 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]' - 2817 | for (destructive_iterator it = ht.destructive_begin(); - | ~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]' - 2948 | _move_from(mover, ht, min_buckets_wanted); - | ^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]' - 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); - | ^~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' - 3278 | if (_resize_delta(1)) - | ^~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here - 264 | duplicateNames[dupInfo.txId].push_back(processedName); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' is deprecated [-Wdeprecated-copy] - 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } - | ^~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' - 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); - | ^~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here - 264 | duplicateNames[dupInfo.txId].push_back(processedName); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]' - 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2817 | for (destructive_iterator it = ht.destructive_begin(); - | ~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2948 | _move_from(mover, ht, min_buckets_wanted); - | ^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); - | ^~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3234:9: required from 'std::pair::ne_iterator, bool> spp::sparse_hashtable::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparsetable::ne_iterator = spp::Two_d_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]' - 3234 | _resize_delta(1); // adding an object, grow if need be - | ^~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:4225:73: required from 'std::pair::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator, bool> spp::sparse_hash_set::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparse_hashtable::const_iterator = spp::Two_d_iterator, const spp::sparsegroup, spp::libc_allocator > >*, const std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]' - 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:490:26: required from here - 490 | auto it = dset.insert(dname); - | ~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] - 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } - | ^~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::__cxx11::basic_string; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::__cxx11::basic_string*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' - 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); - | ^~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here - 264 | duplicateNames[dupInfo.txId].push_back(processedName); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp:2: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp:35: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': @@ -2782,128 +2919,15 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp -[ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/metro/metrohash64.cpp -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5: -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]' - 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2817 | for (destructive_iterator it = ht.destructive_begin(); - | ~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2948 | _move_from(mover, ht, min_buckets_wanted); - | ^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); - | ^~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3278 | if (_resize_delta(1)) - | ^~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' - 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; - | ~~~~~~~~~~~~~~~~~~^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here - 466 | template class RefSeqConstructor; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] - 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } - | ^~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' - 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); - | ^~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' - 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; - | ~~~~~~~~~~~~~~~~~~^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here - 466 | template class RefSeqConstructor; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' - 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; - | ~~~~~~~~~~~~~~~~~~^ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here - 466 | template class RefSeqConstructor; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ +[ 68%] Linking CXX static library libgraphdump.a +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 +/usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o +/usr/bin/ranlib libgraphdump.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +[ 68%] Built target graphdump [ 69%] Linking CXX static library libalevin_core.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 -"/usr/bin/gcc-ar-14" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -"/usr/bin/gcc-ranlib-14" libalevin_core.a -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 69%] Built target alevin_core -[ 70%] Linking CXX static library libsalmon_core.a -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 -"/usr/bin/gcc-ar-14" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -"/usr/bin/gcc-ranlib-14" libsalmon_core.a -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 70%] Built target salmon_core In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/sha2.hpp:9, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:27: @@ -3129,32 +3153,51 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 60 into object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ -[ 71%] Linking CXX static library libUnitTestsMain.a +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 +"/usr/bin/gcc-ar-14" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o +"/usr/bin/gcc-ranlib-14" libalevin_core.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +[ 69%] Built target alevin_core +[ 70%] Linking CXX static library libsalmon_core.a +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 +"/usr/bin/gcc-ar-14" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o +"/usr/bin/gcc-ranlib-14" libsalmon_core.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +[ 70%] Built target salmon_core +[ 71%] Linking CXX static library libpuffer.a +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 +[ 72%] Linking CXX static library libUnitTestsMain.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.dir/link.txt --verbose=1 /usr/bin/ar qc libUnitTestsMain.a CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o /usr/bin/ranlib libUnitTestsMain.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 71%] Built target UnitTestsMain +[ 72%] Built target UnitTestsMain make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend make[4]: Entering directory 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-I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp -[ 73%] Building CXX object 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-DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp +/usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o +/usr/bin/ranlib libpuffer.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' +[ 76%] Built target puffer In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp:6: + from /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp:6: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3167,7 +3210,7 @@ from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp:6: + from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3180,7 +3223,7 @@ from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12: + from /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp:6: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3189,13 +3232,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 76%] Linking CXX static library libpuffer.a -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 -/usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o 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--verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/unitTests.dir/link.d CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -o unitTests -L/build/reproducible-path/salmon-1.10.2+ds1/lib -L/build/reproducible-path/salmon-1.10.2+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_timer.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 @@ -3216,46 +3252,54 @@ make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' -[ 79%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o +[ 82%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o +[ 82%] 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-I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops 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-funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Alevin.cpp.o -MF CMakeFiles/salmon.dir/Alevin.cpp.o.d -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish 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-I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops 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-I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp +cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -MF CMakeFiles/salmon.dir/BAMUtils.cpp.o.d -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/BAMUtils.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_random.hpp:104, from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp:22: /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] @@ -3266,19 +3310,6 @@ | ^~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/include/ProgramOptionsGenerator.hpp:5, - from /build/reproducible-path/salmon-1.10.2+ds1/src/ProgramOptionsGenerator.cpp:4: -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/WhiteList.hpp:14, @@ -3291,13 +3322,10 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentCommon.hpp:10, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentModel.hpp:6, - from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:8: + from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3320,7 +3348,9 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp:29: + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/include/ProgramOptionsGenerator.hpp:5, + from /build/reproducible-path/salmon-1.10.2+ds1/src/ProgramOptionsGenerator.cpp:4: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3343,11 +3373,9 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, - from /build/reproducible-path/salmon-1.10.2+ds1/src/GZipWriter.cpp:9: + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentCommon.hpp:10, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentModel.hpp:6, + from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:8: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3385,8 +3413,8 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11, - from /build/reproducible-path/salmon-1.10.2+ds1/src/Salmon.cpp:49: + from /build/reproducible-path/salmon-1.10.2+ds1/include/ONTAlignmentModel.hpp:9, + from /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:11: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3408,9 +3436,8 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12: + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11, + from /build/reproducible-path/salmon-1.10.2+ds1/src/BuildSalmonIndex.cpp:34: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3436,11 +3463,7 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8, - from /build/reproducible-path/salmon-1.10.2+ds1/include/EMUtils.hpp:6, - from /build/reproducible-path/salmon-1.10.2+ds1/src/EMUtils.cpp:1: + from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp:29: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3451,8 +3474,9 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11, - from /build/reproducible-path/salmon-1.10.2+ds1/src/BuildSalmonIndex.cpp:34: + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, + from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3463,7 +3487,11 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:75: + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, + from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8, + from /build/reproducible-path/salmon-1.10.2+ds1/include/EMUtils.hpp:6, + from /build/reproducible-path/salmon-1.10.2+ds1/src/EMUtils.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3472,8 +3500,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, @@ -3491,6 +3517,17 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:75: +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:76: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} @@ -3502,8 +3539,26 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/ONTAlignmentModel.hpp:9, - from /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:11: + from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, + from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp:33: +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, + from /build/reproducible-path/salmon-1.10.2+ds1/src/GZipWriter.cpp:9: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3512,20 +3567,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'AlignmentModel::AlnModelProb AlignmentModel::logLikelihood(bam_seq_t*, bam_seq_t*, Transcript&, std::vector >&)': -/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:96:33: warning: unused parameter 'primary' [-Wunused-parameter] - 96 | bam_seq_t* read, bam_seq_t* primary, Transcript& ref, - | ~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const ReadPair&, const ReadPair&, Transcript&)': -/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:230:75: warning: unused parameter 'primary' [-Wunused-parameter] - 230 | double AlignmentModel::logLikelihood(const ReadPair& hit, const ReadPair& primary, Transcript& ref) { - | ~~~~~~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'void AlignmentModel::update(const ReadPair&, const ReadPair&, Transcript&, double, double)': -/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter] - 429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary, - | ~~~~~~~~~~~~~~~~^~~~~~~ -[ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, @@ -3545,8 +3586,8 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentCommon.hpp:10, - from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp:1: + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11, + from /build/reproducible-path/salmon-1.10.2+ds1/src/Salmon.cpp:49: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3555,6 +3596,22 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In constructor 'ONTAlignmentModel::ONTAlignmentModel(double, uint32_t)': +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter 'alpha' [-Wunused-parameter] + 17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins) + | ~~~~~~~^~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'double ONTAlignmentModel::logLikelihood(const UnpairedRead&, const UnpairedRead&, Transcript&)': +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:53:22: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] + 53 | if(counts.sclips() >= cigarRLen) + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::update(const UnpairedRead&, const UnpairedRead&, Transcript&, double, double)': +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:137:56: warning: unused parameter 'p' [-Wunused-parameter] + 137 | Transcript& ref, double p, double mass) { + | ~~~~~~~^ +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::printModel(std::ostream&)': +/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:194:50: warning: unused parameter 'os' [-Wunused-parameter] + 194 | void ONTAlignmentModel::printModel(std::ostream& os) { + | ~~~~~~~~~~~~~~^~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' @@ -3705,24 +3762,27 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -MF CMakeFiles/salmon.dir/BAMUtils.cpp.o.d -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/BAMUtils.cpp -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In constructor 'ONTAlignmentModel::ONTAlignmentModel(double, uint32_t)': -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter 'alpha' [-Wunused-parameter] - 17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins) - | ~~~~~~~^~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'double ONTAlignmentModel::logLikelihood(const UnpairedRead&, const UnpairedRead&, Transcript&)': -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:53:22: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 53 | if(counts.sclips() >= cigarRLen) - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::update(const UnpairedRead&, const UnpairedRead&, Transcript&, double, double)': -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:137:56: warning: unused parameter 'p' [-Wunused-parameter] - 137 | Transcript& ref, double p, double mass) { - | ~~~~~~~^ -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::printModel(std::ostream&)': -/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:194:50: warning: unused parameter 'os' [-Wunused-parameter] - 194 | void ONTAlignmentModel::printModel(std::ostream& os) { - | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'AlignmentModel::AlnModelProb AlignmentModel::logLikelihood(bam_seq_t*, bam_seq_t*, Transcript&, std::vector >&)': +/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:96:33: warning: unused parameter 'primary' [-Wunused-parameter] + 96 | bam_seq_t* read, bam_seq_t* primary, Transcript& ref, + | ~~~~~~~~~~~^~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const ReadPair&, const ReadPair&, Transcript&)': +/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:230:75: warning: unused parameter 'primary' [-Wunused-parameter] + 230 | double AlignmentModel::logLikelihood(const ReadPair& hit, const ReadPair& primary, Transcript& ref) { + | ~~~~~~~~~~~~~~~~^~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'void AlignmentModel::update(const ReadPair&, const ReadPair&, Transcript&, double, double)': +/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter] + 429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary, + | ~~~~~~~~~~~~~~~~^~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:60: +/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp: In function 'void alevin::model::coinTossBarcodeModel(std::string, const std::vector >&, MapT&)': +/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: warning: loop variable 'trueBarcode' creates a copy from type 'const std::string' {aka 'const std::__cxx11::basic_string'} [-Wrange-loop-construct] + 168 | for(const std::string trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: note: use reference type to prevent copying + 168 | for(const std::string trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': @@ -3831,15 +3891,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:60: -/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp: In function 'void alevin::model::coinTossBarcodeModel(std::string, const std::vector >&, MapT&)': -/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: warning: loop variable 'trueBarcode' creates a copy from type 'const std::string' {aka 'const std::__cxx11::basic_string'} [-Wrange-loop-construct] - 168 | for(const std::string trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: note: use reference type to prevent copying - 168 | for(const std::string trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': @@ -3948,6 +3999,468 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::DropSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1084:23: required from here + 1084 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1085 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1086 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::InDropV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::InDropV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1094:25: required from here + 1094 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1095 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1096 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CITESeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CITESeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1110:25: required from here + 1110 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1111 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1112 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::ChromiumV3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::ChromiumV3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1122:23: required from here + 1122 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1123 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1124 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Chromium; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Chromium; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1129:23: required from here + 1129 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1130 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1131 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Gemcode; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Gemcode; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1136:23: required from here + 1136 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1137 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1138 | unmateFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1143:23: required from here + 1143 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1144 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1145 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1150:23: required from here + 1150 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1151 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1152 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV1; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV1; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1157:23: required from here + 1157 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1158 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1159 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1164:23: required from here + 1164 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1165 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1166 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::QuartzSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::QuartzSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1171:23: required from here + 1171 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1172 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1173 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SciSeq3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SciSeq3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1177:23: required from here + 1177 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1178 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1179 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Custom; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Custom; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1183:23: required from here + 1183 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1184 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1185 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CustomGeometry; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CustomGeometry; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' + 938 | processBarcodes(barcodeFiles, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + 939 | readFiles, + | ~~~~~~~~~~ + 940 | aopt, + | ~~~~~ + 941 | barcodeSoftMap, + | ~~~~~~~~~~~~~~~ + 942 | trueBarcodes, + | ~~~~~~~~~~~~~ + 943 | freqCounter, + | ~~~~~~~~~~~~ + 944 | numLowConfidentBarcode); + | ~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1189:23: required from here + 1189 | initiatePipeline(aopt, sopt, orderedOptions, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1190 | vm, commentString, noTgMap, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1191 | barcodeFiles, readFiles, salmonIndex); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying + 488 | for (const auto trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' @@ -3974,6 +4487,8 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -4024,6 +4539,106 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here + 12 | txpIdxMap[ transcripts[i] ] = i; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -4049,6 +4664,81 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here + 35 | txpToGeneMap[tid] = gid; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here + 98 | barcodeMap[i] = i; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = long unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>; reference = std::pair, long unsigned int>&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here + 105 | trueBarcodeMap[bc] = idx; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type' {aka 'std::pair, long unsigned int>'} to 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference' {aka 'std::pair, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = long unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -4233,12 +4923,13 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10: -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -4257,13 +4948,16 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -4282,9 +4976,121 @@ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here + 12 | txpIdxMap[ transcripts[i] ] = i; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here + 35 | txpToGeneMap[tid] = gid; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here + 98 | barcodeMap[i] = i; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = long unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -4313,6 +5119,34 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; mutable_value_type = std::pair, long unsigned int>; reference = std::pair, long unsigned int>&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here + 105 | trueBarcodeMap[bc] = idx; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type' {aka 'std::pair, long unsigned int>'} to 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference' {aka 'std::pair, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = long unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; mutable_value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -4459,31 +5293,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:65: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator::reallocate(pointer, size_t) [with T = std::pair, unsigned int>; pointer = std::pair, unsigned int>*; size_t = long unsigned int]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' @@ -4573,922 +5382,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here - 12 | txpIdxMap[ transcripts[i] ] = i; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here - 35 | txpToGeneMap[tid] = gid; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here - 98 | barcodeMap[i] = i; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = long unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>; reference = std::pair, long unsigned int>&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here - 105 | trueBarcodeMap[bc] = idx; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type' {aka 'std::pair, long unsigned int>'} to 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference' {aka 'std::pair, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = long unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here - 12 | txpIdxMap[ transcripts[i] ] = i; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here - 35 | txpToGeneMap[tid] = gid; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here - 98 | barcodeMap[i] = i; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = long unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; mutable_value_type = std::pair, long unsigned int>; reference = std::pair, long unsigned int>&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here - 105 | trueBarcodeMap[bc] = idx; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type' {aka 'std::pair, long unsigned int>'} to 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference' {aka 'std::pair, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = long unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::DropSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1084:23: required from here - 1084 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1085 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1086 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::InDropV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::InDropV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1094:25: required from here - 1094 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1095 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1096 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CITESeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CITESeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1110:25: required from here - 1110 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1111 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1112 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::ChromiumV3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::ChromiumV3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1122:23: required from here - 1122 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1123 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1124 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Chromium; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Chromium; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1129:23: required from here - 1129 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1130 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1131 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Gemcode; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Gemcode; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1136:23: required from here - 1136 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1137 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1138 | unmateFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1143:23: required from here - 1143 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1144 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1145 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1150:23: required from here - 1150 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1151 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1152 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV1; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV1; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1157:23: required from here - 1157 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1158 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1159 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1164:23: required from here - 1164 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1165 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1166 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::QuartzSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::QuartzSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1171:23: required from here - 1171 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1172 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1173 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SciSeq3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SciSeq3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1177:23: required from here - 1177 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1178 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1179 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Custom; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Custom; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1183:23: required from here - 1183 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1184 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1185 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, - from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7: -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CustomGeometry; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CustomGeometry; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' - 938 | processBarcodes(barcodeFiles, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ - 939 | readFiles, - | ~~~~~~~~~~ - 940 | aopt, - | ~~~~~ - 941 | barcodeSoftMap, - | ~~~~~~~~~~~~~~~ - 942 | trueBarcodes, - | ~~~~~~~~~~~~~ - 943 | freqCounter, - | ~~~~~~~~~~~~ - 944 | numLowConfidentBarcode); - | ~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1189:23: required from here - 1189 | initiatePipeline(aopt, sopt, orderedOptions, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1190 | vm, commentString, noTgMap, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1191 | barcodeFiles, readFiles, salmonIndex); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying - 488 | for (const auto trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here - 747 | arboFragCounts[gid][it.first] += it.second; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -5597,36 +5490,9 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10, + from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:58: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -5677,62 +5543,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here - 747 | arboFragCounts[gid][it.first] += it.second; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here - 1426 | size_t numLowConfidentBarcode); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -5841,37 +5651,60 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, + from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7, + from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonMappingUtils.hpp:44, + from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:93: +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here - 1426 | size_t numLowConfidentBarcode); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::InDropV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -5977,49 +5810,9 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp:33: -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6074,6 +5867,31 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6128,58 +5946,29 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, - from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7, - from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonMappingUtils.hpp:44, - from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:93: -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': @@ -6344,31 +6133,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6423,6 +6187,62 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6531,34 +6351,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6613,32 +6405,32 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': @@ -6695,6 +6487,34 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV1; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6746,6 +6566,34 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ @@ -6803,34 +6651,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6885,6 +6705,34 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6939,62 +6787,6 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -7103,34 +6895,58 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, + from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7: +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -7455,9 +7271,33 @@ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47, - from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10, - from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:58: +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, + from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -7508,6 +7348,87 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here + 747 | arboFragCounts[gid][it.first] += it.second; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -7533,6 +7454,90 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here + 747 | arboFragCounts[gid][it.first] += it.second; + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here + 1426 | size_t numLowConfidentBarcode); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -7589,6 +7594,37 @@ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here + 1426 | size_t numLowConfidentBarcode); + | ^ +/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -8134,12 +8170,12 @@ preparing documents... done copying assets... copying static files... -Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/language_data.js -Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/documentation_options.js -Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js +Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/basic.css +Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/classic.css Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js +Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js copying static files: done copying extra files... copying extra files: done @@ -8193,9 +8229,9 @@ 1: Test timeout computed to be: 10000000 1: -- For unit tests, will set working directory to /build/reproducible-path/salmon-1.10.2+ds1/tests 1: =============================================================================== -1: All tests passed (1996327 assertions in 4 test cases) +1: All tests passed (1977897 assertions in 4 test cases) 1: -1/2 Test #1: unit_tests ....................... Passed 1.06 sec +1/2 Test #1: unit_tests ....................... Passed 0.22 sec test 2 Start 2: salmon_read_test_quasi @@ -8208,18 +8244,18 @@ 2: sample_data/transcripts.fasta 2: sample_data/reads_1.fastq 2: index ["sample_salmon_quasi_index"] did not previously exist . . . creating it -2: [2025-03-14 09:17:43.678] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode. -2: [2025-03-14 09:17:43.678] [jLog] [info] building index +2: [2026-04-17 17:45:46.861] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode. +2: [2026-04-17 17:45:46.861] [jLog] [info] building index 2: out : sample_salmon_quasi_index -2: [2025-03-14 09:17:43.678] [puff::index::jointLog] [info] Running fixFasta +2: [2026-04-17 17:45:46.861] [puff::index::jointLog] [info] Running fixFasta 2: 2: [Step 1 of 4] : counting k-mers 2: -2: [2025-03-14 09:17:43.701] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides -2: [2025-03-14 09:17:43.701] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts +2: [2026-04-17 17:45:46.864] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides +2: [2026-04-17 17:45:46.864] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts 2: wrote 15 cleaned references -2: [2025-03-14 09:17:43.702] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers -2: [2025-03-14 09:17:43.703] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20 +2: [2026-04-17 17:45:46.865] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers +2: [2026-04-17 17:45:46.866] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20 2: Threads = 2 2: Vertex length = 31 2: Hash functions = 5 @@ -8235,7 +8271,7 @@ 2: True junctions count = 14 2: False junctions count = 18 2: Hash table size = 32 -2: Candidate marks count = 57 +2: Candidate marks count = 56 2: -------------------------------------------------------------------------------- 2: Reallocating bifurcations time: 0 2: True marks count: 51 @@ -8253,44 +8289,44 @@ 2: (prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0 2: contig count: 24 element count: 19592 complex nodes: 0 2: # of ones in rank vector: 23 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index 2: size = 19592 2: ----------------------------------------- -2: | Loading contigs | Time = 100.87 us +2: | Loading contigs | Time = 77.752 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- -2: | Loading contig boundaries | Time = 57.921 us +2: | Loading contig boundaries | Time = 53.195 us 2: ----------------------------------------- 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: 23 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] contig count for validation: 23 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Total # of Contigs : 23 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Total # of contig vec entries: 36 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] bits per offset entry 6 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Done constructing the contig vector. 24 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] # segments = 23 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] total length = 19,592 -2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Reading the reference files ... -2: [2025-03-14 09:17:43.860] [puff::index::jointLog] [info] positional integer width = 15 -2: [2025-03-14 09:17:43.860] 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0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec -2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] mphf size = 0.0125198 MB -2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] chunk size = 9,796 -2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] chunk 0 = [0, 9,796) -2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562) -2: [2025-03-14 09:17:44.203] [puff::index::jointLog] [info] finished populating pos vector -2: [2025-03-14 09:17:44.203] [puff::index::jointLog] [info] writing index components -2: [2025-03-14 09:17:44.204] [puff::index::jointLog] [info] finished writing dense pufferfish index -2: [2025-03-14 09:17:44.205] [jLog] [info] done building index +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] contig count for validation: 23 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Total # of Contigs : 23 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Total # of contig vec entries: 36 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] bits per offset entry 6 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Done constructing the contig vector. 24 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] # segments = 23 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] total length = 19,592 +2: [2026-04-17 17:45:46.886] [puff::index::jointLog] [info] Reading the reference files ... +2: [2026-04-17 17:45:46.887] [puff::index::jointLog] [info] positional integer width = 15 +2: [2026-04-17 17:45:46.887] [puff::index::jointLog] [info] seqSize = 19,592 +2: [2026-04-17 17:45:46.887] [puff::index::jointLog] [info] rankSize = 19,592 +2: [2026-04-17 17:45:46.887] [puff::index::jointLog] [info] edgeVecSize = 0 +2: [2026-04-17 17:45:46.887] [puff::index::jointLog] [info] num keys = 18,902 +2: [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 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[puff::index::jointLog] [info] mphf size = 0.0125198 MB +2: [2026-04-17 17:45:46.901] [puff::index::jointLog] [info] chunk size = 9,796 +2: [2026-04-17 17:45:46.901] [puff::index::jointLog] [info] chunk 0 = [0, 9,796) +2: [2026-04-17 17:45:46.901] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562) +2: [2026-04-17 17:45:46.902] [puff::index::jointLog] [info] finished populating pos vector +2: [2026-04-17 17:45:46.902] [puff::index::jointLog] [info] writing index components +2: [2026-04-17 17:45:46.903] [puff::index::jointLog] [info] finished writing dense pufferfish index +2: [2026-04-17 17:45:46.903] [jLog] [info] done building index 2: for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 2: Bitarray 105024 bits (100.00 %) (array + ranks ) 2: final hash 0 bits (0.00 %) (nb in final hash 0) @@ -8303,58 +8339,56 @@ 2: ### [ mates2 ] => { reads_2.fastq } 2: ### [ output ] => { sample_salmon_quasi_quant } 2: Logs will be written to sample_salmon_quasi_quant/logs +2: [2026-04-17 17:45:46.941] [jointLog] [info] setting maxHashResizeThreads to 42 2: ----------------------------------------- -2: | Loading contig table | Time = 61.742 us +2: | Loading contig table | Time = 26.11 us 2: ----------------------------------------- 2: size = 24 2: ----------------------------------------- -2: | Loading contig offsets | Time = 95.196 us +2: | Loading contig offsets | Time = 79.3 us 2: ----------------------------------------- 2: ----------------------------------------- -2: | Loading reference lengths | Time = 8.882 us +2: | Loading reference lengths | Time = 9.715 us 2: ----------------------------------------- 2: ----------------------------------------- -2: | Loading mphf table | Time = 90.956 us +2: | Loading mphf table | Time = 60.273 us 2: ----------------------------------------- 2: size = 19592 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: ----------------------------------------- -2: | Loading contig boundaries | Time = 122.24 us +2: | Loading contig boundaries | Time = 136.04 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- -2: | Loading sequence | Time = 68.701 us +2: | Loading sequence | Time = 75.801 us 2: ----------------------------------------- 2: size = 18902 2: ----------------------------------------- -2: | Loading positions | Time = 134.73 us +2: | Loading positions | Time = 112.36 us 2: ----------------------------------------- 2: size = 28562 2: ----------------------------------------- -2: | Loading reference sequence | Time = 64.912 us +2: | Loading reference sequence | Time = 69.401 us 2: ----------------------------------------- 2: ----------------------------------------- -2: | Loading reference accumulative lengths | Time = 8.9 us +2: | Loading reference accumulative lengths | Time = 8.139 us 2: ----------------------------------------- -2: [2025-03-14 09:17:44.359] [jointLog] [info] setting maxHashResizeThreads to 20 -2: [2025-03-14 09:17:44.359] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. -2: [2025-03-14 09:17:44.359] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 -2: [2025-03-14 09:17:44.359] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. -2: [2025-03-14 09:17:44.359] [jointLog] [info] parsing read library format -2: [2025-03-14 09:17:44.359] [jointLog] [info] There is 1 library. -2: [2025-03-14 09:17:44.359] [jointLog] [info] Loading pufferfish index -2: [2025-03-14 09:17:44.359] [jointLog] [info] Loading dense pufferfish index. -2: [2025-03-14 09:17:44.360] [jointLog] [info] done +2: [2026-04-17 17:45:46.941] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. +2: [2026-04-17 17:45:46.941] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 +2: [2026-04-17 17:45:46.941] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. +2: [2026-04-17 17:45:46.941] [jointLog] [info] parsing read library format +2: [2026-04-17 17:45:46.941] [jointLog] [info] There is 1 library. +2: [2026-04-17 17:45:46.941] [jointLog] [info] Loading pufferfish index +2: [2026-04-17 17:45:46.941] [jointLog] [info] Loading dense pufferfish index. +2: [2026-04-17 17:45:46.942] [jointLog] [info] done +2: [2026-04-17 17:45:46.996] [jointLog] [info] Index contained 15 targets +2: [2026-04-17 17:45:46.996] [jointLog] [info] Number of decoys : 0 2: 2: 2: 2: -2: [2025-03-14 09:17:44.612] [jointLog] [info] Index contained 15 targets -2: [2025-03-14 09:17:44.612] [jointLog] [info] Number of decoys : 0 -2: [2025-03-14 09:17:45.174] [jointLog] [info] Computed 28 rich equivalence classes for further processing -2: [2025-03-14 09:17:45.175] [jointLog] [info] Counted 10,000 total reads in the equivalence classes 2: 2: 2: @@ -8363,29 +8397,31 @@ 2: 2: 2: -2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of mappings discarded because of alignment score : 67 -2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0 -2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 -2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0 -2: [2025-03-14 09:17:45.208] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000. +2: [2026-04-17 17:45:47.207] [jointLog] [info] Computed 28 rich equivalence classes for further processing +2: [2026-04-17 17:45:47.207] [jointLog] [info] Counted 10,000 total reads in the equivalence classes +2: [2026-04-17 17:45:47.221] [jointLog] [info] Number of mappings discarded because of alignment score : 67 +2: [2026-04-17 17:45:47.221] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0 +2: [2026-04-17 17:45:47.221] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 +2: [2026-04-17 17:45:47.221] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0 +2: [2026-04-17 17:45:47.221] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000. 2: The effective lengths have been computed using the observed mappings. 2: -2: [2025-03-14 09:17:45.208] [jointLog] [info] Mapping rate = 100% +2: [2026-04-17 17:45:47.221] [jointLog] [info] Mapping rate = 100% 2: -2: [2025-03-14 09:17:45.208] [jointLog] [info] finished quantifyLibrary() -2: [2025-03-14 09:17:45.208] [jointLog] [info] Starting optimizer -2: [2025-03-14 09:17:45.209] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate -2: [2025-03-14 09:17:45.209] [jointLog] [info] iteration = 0 | max rel diff. = 14.87 -2: [2025-03-14 09:17:45.211] [jointLog] [info] iteration = 100 | max rel diff. = 3.31285e-05 -2: [2025-03-14 09:17:45.211] [jointLog] [info] Finished optimizer -2: [2025-03-14 09:17:45.211] [jointLog] [info] writing output +2: [2026-04-17 17:45:47.221] [jointLog] [info] finished quantifyLibrary() +2: [2026-04-17 17:45:47.329] [jointLog] [info] Starting optimizer +2: [2026-04-17 17:45:47.330] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate +2: [2026-04-17 17:45:47.330] [jointLog] [info] iteration = 0 | max rel diff. = 14.87 +2: [2026-04-17 17:45:47.331] [jointLog] [info] iteration = 100 | max rel diff. = 3.96731e-05 +2: [2026-04-17 17:45:47.331] [jointLog] [info] Finished optimizer +2: [2026-04-17 17:45:47.331] [jointLog] [info] writing output 2: 2: Salmon (read) ran successfully -2/2 Test #2: salmon_read_test_quasi ........... Passed 2.55 sec +2/2 Test #2: salmon_read_test_quasi ........... Passed 1.66 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 3.61 sec +Total Test time (real) = 2.11 sec make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' create-stamp debian/debhelper-build-stamp @@ -8393,7 +8429,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_auto_install - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/salmon-1.10.2\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/salmon-1.10.2\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -8424,28 +8460,28 @@ ========================================================================== make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' rm -Rvf /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib -removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a' -removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libgraphdump.a' -removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake' +removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard' -removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libtwopaco.a' -removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake' +removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' +removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' +removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco' +removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libgraphdump.a' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake' +removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libntcard.a' -removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' -removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' -removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco' +removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libtwopaco.a' +removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib' make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_install dh_installdocs dh_sphinxdoc -dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.js -dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/themetoggle.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/search-focus.js +dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.js +dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js dh_installchangelogs dh_installexamples dh_installman @@ -8476,12 +8512,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1496209/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1830931 and its subdirectories -I: Current time: Fri Mar 14 09:19:15 -12 2025 -I: pbuilder-time-stamp: 1741987155 +I: removing directory /srv/workspace/pbuilder/1496209 and its subdirectories +I: Current time: Fri Apr 17 17:46:35 +14 2026 +I: pbuilder-time-stamp: 1776397595